Selective logging is a widely extended forestry practice that affects tree populations by changing their spatial structure. As most tropical timber tree species are animal-pollinated, selective logging increase the average distance between conspecific trees and hereby affect the guild of pollinators and gene flow between the standing trees. In order to study the effects of logging on the population genetics of tropical timber tree species, we assessed selfing rates, genetic diversity, effective number of pollen donors and effective distances of pollination in progenies collected in a recently logged plot and a un-logged-control plot of Guibourtia chodatiana (Hassl.). We found outcrossing rates close to one, even in the logged plot where the density had been reduced to 55%. Mean expected heterozygosity was almost identical in the logged and un-logged plots (He Control = 0.38 ± 0.20 SD; He Logged = 0.41 ± 0.21 SD) and genetic differentiation between plots was very low (Fst = 0.03). The logged population had a slightly higher effective number of pollen donors compared to the control (Nep Logged = 12.5; Nep Control = 10, respectively). However, the fruit set was almost twice in the control than in the logged plot. This finding suggests that there could be a pollinator limitation leading to reduction of fertilized ovules (i.e. fruits) in the logged plot. However, the larger distances of pollination in the logged than in the control plot (under the assumption of normal and negative exponential distributions) suggest that pollinators could bridge the inter-tree distances, despite the occurrence of logging.